[gmx-users] "B" state for free energy corrupts minimization?

Berk Hess gmx3 at hotmail.com
Thu Feb 2 09:15:16 CET 2006

>From: mernst at tricity.wsu.edu
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] "B" state for free energy corrupts minimization?
>Date: Wed, 1 Feb 2006 23:46:45 -0800 (PST)
> >Indeed the zeros in the bonds (and probably also in the angles?) are the
> >problem.
> >This is caused by a bug that I have fixed in November,
> >but we did not release 3.3.1 yet:
> >http://www.gromacs.org/pipermail/gmx-revision/2005-November/000117.html
> >
> >Apparently some bonded interaction parameters are not defined
> >for bonded interactions that involve your 36 atom type in the B-state.
> >
> >You should add parameters for these bonded interactions,
> >either directly after the definition of the bonded interaction,
> >or in the force-field bondtypes and angletypes sections.
> >
> >Berk.
>Thank you for the hint. I was able to fix the zeros in the bonds, but I am 
>trouble tracking down the source of the zeros in the angles. Which file or 
>files needed
>modification to fix this bug? I have been using 3.3. I tried downloading 
>the source and
>building from CVS, but it failed:

I would not try to change the source code, or use the CVS source.
The fix in CVS would produce the tpr file you want,
but it does not fix the actual source of the problem,
which is that you do not have parameters in the forcefield
for some bonded interactions in the B-state.

You a probably only missing one or two angle parameters
in the forcefield.
You should look in the ff...bon.itp file for your forcefield.
Go to the angletypes section and copy the lines for
the original atomtype and replace the original atomtype
in the copy by 36.


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